Doktoratskolleg MEIBio - Molecular and Elemental Imaging in Bioscience
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PhD Fellow #1: Alexander Reismann

Optical microscopy on brain sections below the diffraction limit

After school, I had to make a decision: What should I study? The three things that interested me most were medicine, biomedical engineering and physics. Without a special reason I chose to start with physics and I don't regret it. Approaching the end of my master studies a new opportunity of combining the three fields of interest opened up: the group of Gerhard Schütz moved to the Vienna University of Technology. Biophysics immediately caught my attention and I started my master thesis in optical super resolution microscopy. During my studies, I came across many other medical imaging methods ranging from the classical X-ray up to 3D/4D ultrasound imaging. New developments and improvements of imaging techniques are of enormous importance for the evolution of medicine in general, but it is getting more and more complicated due to growing requirements evoked by natural borders physic implies on us. In research, there is a need for higher resolution, higher contrast and faster methods. In clinical application, the focus is on cheap, fast and especially safe techniques. The combination of these two fields makes it so interesting to me. When I first heard of MEIBio I instantly knew, that this PhD is as interdisciplinary as it gets. Since I already worked in the field of optical microscopy I know that the combination of two state of the art microscopy techniques and using them on biological samples is an interesting and important task. Coming from physics the construction of a new microscope is a useful test of my education. I am looking forward to this exciting three years of science.

PhD Fellow #2:

Increasing the resolution in whole brain imaging


PhD Fellow #3: Jonas Ramoni

Quantitative mapping of localized cellulase expression and secretion in the functionally stratified fungal colony by combined mass spectrometry and live-cell imaging

My fascination for microorganisms and their tremendous potential to solve problems of modern society started early in school. Besides their application in the pharmaceutical industry I was especially interested in their use in the green and white biotechnology sector. This interest was the reason why I chose to study molecular biotechnology, a study where I learned how to handle and improve various kinds of microorganisms so that they fulfill specific requirements for their future application. I was able to gain deep insights into cultivation and genetic engineering of two of the industrially most relevant organisms, Saccharomyces cerevisiae and Escherichia coli, during a five month research stay at the Stockholm University.For my master studies I switched to University of Vienna to deepen my knowledge in the field of genetics, to further improve my skills in genetic engineering and improvement of microorganisms.For my master thesis I chose to switch from S. cerevisiae to another industrially used organism, the filamentous fungus Trichoderma reesei. My solid theoretical and practical gained knowledge in genetic engineering and handling of microorganisms facilitated the work with the new organism a lot and many aspects appeared to be comparable between the unicellular and the filamentous fungus. Nevertheless, many things were of crucial difference in T.reesei and I was able to learn new techniques especially in the field of protein biochemistry and transcriptional regulation. My reasons for the application to the announced PhD fellow #3 in the program of molecular and elemental imaging in biosciences are diverse. I am firstly convinced that the proposed technique will significantly improve the understanding of how, where and why enzymes are secreted and interact with each other. This in turn will lead to further possibilities to improve the process of enzymatic biopolymer hydrolysis. Furthermore, I see myself very qualified in the field of genetic optimization of industrially used strains, but however, I also see bioanalytics for quantification of this optimization as a prerequisite for a successful career within the industrial biotechnological field.I am therefore highly interested and motivated to learn how to handle mass spectrometry which I see as the most powerful tool to fulfill this prerequisite. A general benefit of the excellence program are the documented and planned collaborations with top scientists and institutes, which will result in significant research synergies and will pave the way for a tight scientific network.

PhD Fellow #4: Anna Balbekova

Photoexpansion Microscopy: Combining Pulsed Mid-IR Laser Spectroscopy With Atomic Force Microscopy

My future carrier will be research oriented and devoted to the development of bioanalytical applications. My scientific interests are bio-analytics, sensing and photonics. For me the “MEIBio” project is a great opportunity to continue my education with a multidisciplinary doctoral program which intersects with the area of my scientific interests, besides it covers areas of my professional confidence. I have applied for this PhD program because it offers opportunity in interdisciplinary research. The most attractive for me is the project devoted to the photoexpansion microscopy, because it allows investigation of biological samples. Besides it implements a spectroscopy technique in which I have a broad experience. Atomic force microscopy is new technique for me and I am looking forward to get new experience. Literature research has shown that the AFM-IR is a new technique which could be improved and it leaves possibilities for new discoveries.

PhD Fellow #5: Maximilian Bonta

Quantification strategies for elemental imaging of biological samples using laser ablation-inductively coupled plasma-mass spectrometry (LA-ICPMS)

The reason I applied for the MEIBio PhD programme is that I am very interested in chemical imaging techniques. Laterally resolved analyses can help to gain deeper insight into processes that cannot be seen using traditional bulk analyses. 'A picture is worth a thousand words' is a proverb said to originate in the Far East and it perfectly expresses the point why imaging is a great way to do chemical investigations. As chemical imaging techniques are still in their infancy and use in daily operations is sure a long way to go in this PhD programme a lot of pioneer work has to be done and to my mind this is the most exciting part of science: taking one of the first steps, improve methods and be able to be part of a constant development. In this context the MEIBio PhD programme gives the unique opportunity to do interdisciplinary work and to connect different working groups and create fruitful synergies. I applied for the position 'Quantification strategies for elemental imaging of biological samples using laser ablation-inductively coupled plasma-mass spectrometry (LA-ICPMS)' because I like the idea of establishing trace elemental analyses in the field of life sciences. Trace elements in tissues can essentially contribute to cellular functions and therefore besides investigations on the molecular level also research on trace elemental information is of great importance. During my Master's Thesis I have already achieved insights to inorganic trace analysis and in this PhD programme I wish to further extend my knowledge in that area of science. Besides the analytical questions I am looking forward to gain experience in medical sciences and other fields of research. Last but not least I hope to find much productive discussion and cooperation with my other PhD colleagues and I am sure also the fun moments in these three years will not go short.

PhD Fellow #6: Florian Brenner

Secondary Ion Mass Spectrometry (SIMS) analysis of bioorganic samples

While I was working in Vienna in a company in the chemical industry, I was introduced to the MEIBio PhD program by a former working colleague at the Institute of Chemical Technologies and Analytics. After working in the industry for almost two years, I allowed myself to rethink my scientific career and concluded that I was not really working as a scientist anymore, which always was a satisfying occupation for me. What really draw my attention, was the combination of typical methods for materials science applied to biological samples and improve the understanding and imaging of so far unknown mechanisms of reactions (e.g. lateral impacts of medication). Another reason for my application was the opportunity to work with several analytical techniques and instruments quite easily as a result of the interdisciplinary character of the PhD program. It is also a good possibility to work with researchers from all over the world and establish contacts for future projects. To give myself interesting and challenging tasks, I decided to apply for the SIMS group, since I had a great background from my diploma thesis, where I could start with some practical work right away, but also combined with new and exciting analytical problems.  

PhD Fellow #7: Anna Turyanskaya

Trace element Distribution in Human Osteoporotic and Non-Osteoporotic Bone using Synchrotron Micro X-Ray Fluorescence Imaging

The idea of continuing my scientific career occupied me ever since I have finished my diploma project, which was carried out at Pharmaceutical Department of Moscow Medical Academy. So after taking a short break (during this period I had been working in the healthcare field and also getting my second university degree) I've finally made up my mind to turn back to science and research. The decision was deliberate therefore and I'd looked through a lot of positions before I've luckily found the MEIBio call announcement. The MEIBio PhD Program drew my attention straight away due to its interdisciplinary character. This prominent feature is of a particular importance to me, since I am unwilling to confine myself within just one research area and rather looking for new knowledge and areas. I value the opportunities to work on compelling relevant topic in collaboration with scientists from various areas of expertise using cutting-age technologies. These appealing aspects of the PhD Program prompted me to apply for it. The project I am now involved in is not only giving me the chance of using my pharmaceutical background but also allowing extending the knowledge of elemental analysis techniques, namely Micro-X-ray Spectrometry. Great work has been done already towards the understanding of the processes leading to such a menacing disease as osteoporosis and I am very pleased to contribute to the further progress of the insight into topic.

PhD Fellow #8: Anastasiya Svirkova

Mass Spectrometry Imaging and Fluorescence Imaging of Polymer Surfaces after Contact with Biological Fluids

I am interested in applied sciences due to opportunity to see results of the researches. TU Wien seems to me to be a place that is fully satisfied this criterion. I am engrossed in investigations that combine different scientific areas. PhD program MEIBio is a multidisciplinary program where people from such scientific fields as chemistry, informatics, biology, physics etc. can work together to solve common questions. For these reasons it is very fascinating for me to be enrolled in DK MEIBio. I have already worked in bioscience, but with another instruments and methods. I suppose to gain new skills and see a great possibility to improve my knowledge in imaging techniques. While choosing a subject of my degree thesis and in the following research topics I was guided by desire to be engaged in science areas that contact with medicine. I am inspired by developments of new materials, methods of diagnostics and visualization, findings of the medical substances. Program MEIBio attracted my attention, because results of these investigations lead to important results in medicine. I chose a project "Mass Spectrometry Imaging and Fluorescence Imaging of Polymers Surfaces after Contact with Biological Fluids" because I feel certain that polymers are now more and more broadly applicable in all areas of human activity. Investigations of artificial materials in medicine are especially important. Considering that such materials are now of great interest, rises a question of studying their in vitro and particularly in vivo properties. For me it is interesting to be engaged in researches of polymers from the point of view of their visualization. Another significant area of this project is a studying of biomolecule (lipid, protein, carbohydrate) behavior. Therefor I have opportunity to achieve more advanced skills and in-depth knowledge of a biochemistry area. I would like to use imaging methods (Mass Spectrometry Imaging and Fluorescence Imaging), which are now considered to be the key technologies.

PhD Fellow #9: Dennis Svatunek

Pretargeted multimodal imaging of cancer - a combined PET and MALDI-based MSI approach

After I started studying chemistry at Vienna University of Technology in 2007 I quickly discovered my passion for organic chemistry as well as analytical chemistry. I then did my bachelor and master thesis in organic synthetic chemistry the field of carbohydrate chemistry.Getting more into carbohydrate chemistry I had the opportunity to attend several inspiring lectures at international symposia, which finally initiated my fascination for chemical biology, especially bioorthogonal ligations with an application to molecular imaging. Molecular imaging, in particular multimodal molecular imaging as well as new imaging methods, is getting more and more in focus of the scientific community, since it is the key for deeper understanding of biologic processes and has an important role in medicine, specially in personalized medicine. The importance of imaging can also be seen by various grants in the field of molecular and medical imaging as well as development of new imaging methods, for example in the Horizon 2020 program by the EU or the FWF. Furthermore the Medical University of Vienna has recently opened a research cluster for medical imaging (Medical Imaging Cluster, MIC)The MEIBio topic "Pretargeted multimodal imaging of cancer - a combined PET and MALDI-based MSI approach" gives me the opportunity to work on a topic in that up-and-coming field. It combines synthetic chemistry with analytical chemistry as well as chemical biology and biomedicine. For me it is very important to work in a multidisciplinary field of research, even if it can be a challenge sometimes.The MEIBio doctoral program is a great program, since it gives the participants the possibility to work in different fields of research, build up a network to different working groups and have easy access to a lot of knowledge, experience and facilities. All these facts have convinced me to apply for the MEIBio program and I am very happy that I can work within this program on a topic I am very interested in.

PhD Fellow #10: Maliheh Assadpour Tehrani

Single Image Registration using Automatic Feature Classification

I finished my biomedical research master project at the Neuroimmonology group of the IDIBAPS Center for Biomedical Research in Barcelona. The main topic of my project is: Diffusion Tensor Imaging study for Multiple Sclerosis in the Optic Radiation. The project involved Image Processing, Visualization and Statistical Analysis of DTI data to find biomarkers for MS disease. Through my master project I found in many challenging application such as for brain imaging, the registration results are often not convincing. Once I have completed my degree, I focused my professional career on the medical image processing especially image registration. I started a project in image processing at CISTIB,UPF , working on Cardiac image processing to gain expertise in image registration, deformable models and integration of different image modalities. Dealing with these projects, I intend to develop a PhD related to image registration issues for applying my technical experience to improve medical image registration and using them for clinical applications. MEIBio could be a great chance for me to develop my scientific and practical abilities. I think it has both freedom of experimental multidisciplinary training along with a high level of academic education.